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galaxy package

Galaxy root package – this is a namespace package.

Subpackages

Submodules

galaxy.app module

class galaxy.app.HaltableContainer[source]

Bases: galaxy.di.Container

__init__() → None[source]
Parameters

container – Optional container if provided the existing definitions will be copied

:param log_undefined_deps indicates if a log message should be emmited when an undefined dep is loaded

haltables: List[Tuple[str, Callable]]
shutdown()[source]
class galaxy.app.SentryClientMixin[source]

Bases: object

configure_sentry_client()[source]
class galaxy.app.MinimalGalaxyApplication(fsmon=False, configure_logging=True, **kwargs)[source]

Bases: galaxy.structured_app.BasicApp, galaxy.config.ConfiguresGalaxyMixin, galaxy.app.HaltableContainer, galaxy.app.SentryClientMixin

Encapsulates the state of a minimal Galaxy application

__init__(fsmon=False, configure_logging=True, **kwargs) → None[source]
Parameters

container – Optional container if provided the existing definitions will be copied

:param log_undefined_deps indicates if a log message should be emmited when an undefined dep is loaded

name: str
config: Any
configure_fluent_log()[source]
application_stack: galaxy.web_stack.ApplicationStack
model: galaxy.model.base.SharedModelMapping
security: galaxy.security.idencoding.IdEncodingHelper
auth_manager: galaxy.auth.AuthManager
toolbox: Any
security_agent: Any
quota_agent: galaxy.quota.QuotaAgent
datatypes_registry: galaxy.datatypes.registry.Registry
class galaxy.app.GalaxyManagerApplication(**kwargs)[source]

Bases: galaxy.structured_app.MinimalManagerApp, galaxy.app.MinimalGalaxyApplication

Extends the MinimalGalaxyApplication with most managers that are not tied to a web or job handling context.

__init__(**kwargs)[source]
Parameters

container – Optional container if provided the existing definitions will be copied

:param log_undefined_deps indicates if a log message should be emmited when an undefined dep is loaded

user_manager: Any
hda_manager: Any
history_manager: Any
dataset_collection_manager: Any
workflow_manager: Any
workflow_contents_manager: Any
library_folder_manager: Any
library_manager: Any
role_manager: Any
file_sources: galaxy.files.ConfiguredFileSources
installed_repository_manager: Any
genome_builds: galaxy.util.dbkeys.GenomeBuilds
class galaxy.app.UniverseApplication(**kwargs)[source]

Bases: galaxy.structured_app.StructuredApp, galaxy.app.GalaxyManagerApplication

Encapsulates the state of a Universe application

__init__(**kwargs) → None[source]
Parameters

container – Optional container if provided the existing definitions will be copied

:param log_undefined_deps indicates if a log message should be emmited when an undefined dep is loaded

amqp_internal_connection_obj: Optional[kombu.connection.Connection]
queue_worker: Any
dependency_resolvers_view: galaxy.tool_util.deps.views.DependencyResolversView
test_data_resolver: galaxy.tool_util.verify.test_data.TestDataResolver
dynamic_tool_manager: Any
api_keys_manager: Any
genomes: Any
data_provider_registry: Any
error_reports: Any
tool_cache: Any
watchers: Any
webhooks_registry: galaxy.webhooks.WebhooksRegistry
security_agent: galaxy.model.security.GalaxyRBACAgent
host_security_agent: galaxy.model.security.HostAgent
workflow_scheduling_manager: Any
trs_proxy: galaxy.workflow.trs_proxy.TrsProxy
interactivetool_manager: Any
tool_shed_repository_cache: Optional[Any]
property is_job_handler
is_webapp: bool
new_installation: bool
tag_handler: galaxy.model.tags.GalaxyTagHandler
file_sources: galaxy.files.ConfiguredFileSources
genome_builds: galaxy.util.dbkeys.GenomeBuilds
job_metrics: galaxy.job_metrics.JobMetrics
model: galaxy.model.mapping.GalaxyModelMapping
install_model: galaxy.model.base.ModelMapping
history_manager: Any
hda_manager: Any
workflow_manager: Any
workflow_contents_manager: Any
library_folder_manager: Any
library_manager: Any
role_manager: Any
tool_data_tables: Any
job_config: Any
installed_repository_manager: Any
job_manager: Any
user_manager: Any
class galaxy.app.StatsdStructuredExecutionTimer(galaxy_statsd_client, *args, **kwds)[source]

Bases: galaxy.util.StructuredExecutionTimer

__init__(galaxy_statsd_client, *args, **kwds)[source]

Initialize self. See help(type(self)) for accurate signature.

to_str(**kwd)[source]
class galaxy.app.ExecutionTimerFactory(config)[source]

Bases: object

__init__(config)[source]

Initialize self. See help(type(self)) for accurate signature.

get_timer(*args, **kwd)[source]

galaxy.config_watchers module

class galaxy.config_watchers.ConfigWatchers(app: galaxy.structured_app.StructuredApp)[source]

Bases: object

Contains ToolConfWatcher, ToolWatcher and ToolDataWatcher objects.

__init__(app: galaxy.structured_app.StructuredApp)[source]

Initialize self. See help(type(self)) for accurate signature.

property watchers
change_state(active)[source]
start()[source]
shutdown()[source]
update_watch_data_table_paths()[source]
property data_manager_configs
property tool_data_paths
property tool_config_paths
property job_rules_paths

galaxy.main module

Entry point for starting Galaxy without starting as part of a web server.

Example Usage: Start a job/workflow handler without a web server and with a given name using.

galaxy-main –server-name handler0

Start as a daemon with (requires daemonized - install with ‘pip install daemonize’):

galaxy-main -d –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –server-name handler0

In daemon mode logging of Galaxy (as opposed to this script) is configured via a loggers section in Galaxy’s ini file - this can be overridden with sensible defaults logging to a single file with the following:

galaxy-main -d –server-name handler0 –daemon-log-file=handler0-daemon.log –pid-file handler0.pid –log-file handler0.log

This can also be used to start Galaxy as a uWSGI mule, e.g. for job handling:

uwsgi … –py-call-osafterfork –mule=lib/galaxy/main.py –mule=lib/galaxy/main.py –farm=job-handlers:1,2

The –py-call-osafterfork allows for proper shutdown on SIGTERM/SIGINT.

galaxy.main.load_galaxy_app(config_builder, config_env=False, log=None, attach_to_pools=None, **kwds)[source]
galaxy.main.handle_signal(signum, frame)[source]
galaxy.main.register_signals()[source]
galaxy.main.app_loop(args, log)[source]
class galaxy.main.GalaxyConfigBuilder(args=None, **kwds)[source]

Bases: object

Generate paste-like configuration from supplied command-line arguments.

__init__(args=None, **kwds)[source]

Initialize self. See help(type(self)) for accurate signature.

classmethod populate_options(arg_parser)[source]
property config_is_ini
app_kwds()[source]
global_conf()[source]
setup_logging()[source]
galaxy.main.main(func=<function app_loop>)[source]

galaxy.queue_worker module

Galaxy control queue and worker. This is used to handle ‘app’ control like reloading the toolbox, etc., across multiple processes.

galaxy.queue_worker.send_local_control_task(app, task, get_response=False, kwargs=None)[source]

This sends a message to the process-local control worker, which is useful for one-time asynchronous tasks like recalculating user disk usage.

galaxy.queue_worker.send_control_task(app, task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]

This sends a control task out to all processes, useful for things like reloading a data table, which needs to happen individually in all processes. Set noop_self to True to not run task for current process. Set get_response to True to wait for and return the task results as a list.

class galaxy.queue_worker.ControlTask(queue_worker)[source]

Bases: object

__init__(queue_worker)[source]

Initialize self. See help(type(self)) for accurate signature.

property connection
property control_queues
property exchange
property declare_queues
on_response(message)[source]
send_task(payload, routing_key, local=False, get_response=False, timeout=10)[source]
galaxy.queue_worker.reconfigure_watcher(app, **kwargs)[source]
galaxy.queue_worker.create_panel_section(app, **kwargs)[source]

Updates in memory toolbox dictionary.

galaxy.queue_worker.reload_tool(app, **kwargs)[source]
galaxy.queue_worker.reload_toolbox(app, save_integrated_tool_panel=True, **kwargs)[source]
galaxy.queue_worker.reload_data_managers(app, **kwargs)[source]
galaxy.queue_worker.reload_display_application(app, **kwargs)[source]
galaxy.queue_worker.reload_sanitize_allowlist(app)[source]
galaxy.queue_worker.recalculate_user_disk_usage(app, **kwargs)[source]
galaxy.queue_worker.reload_tool_data_tables(app, **kwargs)[source]
galaxy.queue_worker.rebuild_toolbox_search_index(app, **kwargs)[source]
galaxy.queue_worker.reload_job_rules(app, **kwargs)[source]
galaxy.queue_worker.reload_core_config(app, **kwargs)[source]
galaxy.queue_worker.reload_tour(app, **kwargs)[source]
galaxy.queue_worker.job_rule_modules(app)[source]
galaxy.queue_worker.admin_job_lock(app, **kwargs)[source]
class galaxy.queue_worker.GalaxyQueueWorker(app, task_mapping=None)[source]

Bases: kombu.mixins.ConsumerProducerMixin, threading.Thread

This is a flexible worker for galaxy’s queues. Each process, web or handler, will have one of these used for dispatching so called ‘control’ tasks.

__init__(app, task_mapping=None)[source]

Initialize self. See help(type(self)) for accurate signature.

send_control_task(task, noop_self=False, get_response=False, routing_key='control.*', kwargs=None)[source]
send_local_control_task(task, get_response=False, kwargs=None)[source]
property declare_queues
bind_and_start()[source]
get_consumers(Consumer, channel)[source]
process_task(body, message)[source]
shutdown()[source]

galaxy.queues module

All message queues used by Galaxy

galaxy.queues.all_control_queues_for_declare(application_stack)[source]

For in-memory routing (used by sqlalchemy-based transports), we need to be able to build the entire routing table in producers.

galaxy.queues.control_queues_from_config(config)[source]

Returns a Queue instance with the correct name and routing key for this galaxy process’s config

galaxy.queues.connection_from_config(config) → Optional[kombu.connection.Connection][source]

galaxy.version module